PaRI’s efforts continued in the extended Affiliate Programme

In early 2020, when the SARS-CoV-2 virus caused a worldwide pandemic, NeIC decided to call for and fund a development project to support pandemic research in the Nordics by enhancing research infrastructure. The project, Nordic Pandemic Research Infrastructure (PaRI), was initiated in November 2020 and ran for one year to help both national and international actors and initiatives working in health research in the Nordics and beyond. The project’s final report has been published on Zenodo.

PaRI was a project that had many external dependencies. The project ended as some important European initiatives were just starting, and the project partners wanted more time to decide on the best approach for transferring some of the results from the project to the partners. Thus, PaRI entered the extended NeIC Affiliate programme to ensure the continued transfer of results and realisation of business benefits. In the extended Affiliate programme, a coordinator is appointed and supported financially by NeIC for one year to oversee this. The contribution percentage of the coordinator is small but it guarantees extra time, a leader and consistency, all of which were much appreciated and essential also in the case of iOBS. The iOBS project piloted the extended Affiliate programme earlier this year with positive experiences and good results (read our article from earlier this year here).

Realised results and contributions to international initiatives

The aim of the PaRI project was to facilitate Nordic research on pandemics, especially the COVID-19 pandemic, by aligning with other European initiatives. It focused on providing guidance on data sharing and infrastructure; provisioning Galaxy portal instances with relevant tools, workflows and data; and setting up a Nordics dashboard of virus variants. Through these efforts the project and its one-year affiliate period contributed to supporting researchers and data producers in pandemic data sharing and analysis. By joining the extended Affiliate programme, the project partners in PaRI committed to continue the collaboration with a strong focus on making sure that the deliverables were well taken care of and that the impact the project had aimed for would be realised. Details of what was achieved during the affiliate period can be read in the recently published affiliate project’s final report.

– Since some important European initiatives were having a slow start as PaRI was already ending, the partners saw the extension as an opportunity to make a few targeted contributions that would push those initiatives forward, says affiliate coordinator Wolmar Nyberg Åkerström.

– During the affiliate period, we were able to provide early input to the BY-COVID project and their Infectious Diseases Toolkit, the ELIXIR-CONVERGE project and their Research Data Management Toolkit (RDMkit), and to EOSC Association’s Task Force on Semantic Interoperability. Joining the affiliate also allowed us to arrange a number of targeted outreach activities and continue a series of meetings between the partners for continued professional exchange around PaRI’s core activities, he continues.

The PaRI-affiliate ended on 31 October. By then, the different technology components used by PaRI were by and large already well maintained by active user and developer communities. The tools and workflows from the PaRI Galaxy instance are available for use in other Galaxy portals and the environment can easily be replicated for projects that require it. The data contributed to the COVID-19 Data Portal is stored and maintained by EMBL-EBI (European Molecular Biology Laboratory’s European Bioinformatics Institute) and the relevant sections of the guidance has been incorporated into the national COVID-19 data portals and contributed to European projects. The PaRI dashboard remains available for use as a demonstrator at ETAIS for the time being.

A small player in a growing, global field

The field of pandemic research has both grown and gained a lot of attention in the past three years. In this wider context, PaRI is a comparably small demonstrator project, but it illustrates some of the major challenges in working with pandemic data. Nyberg Åkerström believes that PaRI has succeeded in aligning well with the European projects and that the solutions that PaRI explored can serve as inspiration for the larger initiatives. The ELIXIR-CONVERGE project which develops best practices for mobilising SARS-CoV-2 genome data, as well as the BY-COVID project which is working towards a framework for making data from infectious diseases open and accessible to everyone, have received early input based on a document The NeIC PaRI partners’ guide to SARS-CoV-2 genome data sharing.

On the global level, WHO (World Health Organization) is taking some measures towards improving the global outbreak surveillance system. The European Health Data Space is a health-specific ecosystem of rules, common standards and practices with focus on primary use (EHDS 1) and also secondary use (EHDS 2) health data, with the aim of providing secure federated access to health data around Europe. In the Nordics, a Nordic Sensitive Data Forum has been established as a community effort driven by the national e-infrastructure providers. The aim is to establish collaboration activities to achieve cross-border federated access and analysis platforms, which can be used for both research and clinical use cases. In addition, the Nordic Commons project aims to test solutions and practical approaches to sharing health data between regional or national actors.

– The results and achievements of the PaRI project and the affiliate period, including tools and guidelines, will be very useful in future activities targeting improving accessibility and reusability of health data, concludes the project owner Abdulrahman Azab.